tbuckley/cabot-search huggingface dataset:
DDDR-07. EVALUATING THE ROLE OF THE PIK3CB PATHWAY IN TEMOZOLOMIDE RESISTANCE IN GLIOBLASTOMA USING THE GENOMICS OF DRUG SENSITIVITY IN CANCER (GDSC) AND CANCER CELL LINE ENCYCLOPEDIA (CCLE) DATABASES
Authors: Leah Huang, Zhi Sheng, Allison Tegge
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma multiforme (GBM) is a lethal primary brain cancer with a median survival of 14.6 months despite standard treatment of maximal surgical resection, radiotherapy, and temozolomide (TMZ). Recent research has identified PIK3CB/p110β as the most important regulator of AKT activation and GBM cell survival. Utilizing the pharmacogenomic databases Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE), we sought to elucidate the relationship between PIK3CB mRNA expression or AKT phosphorylation and GBM treatment resistance. We first identified cell lines with matched PI3K isoform mRNA expression, protein expression (AKT phosphorylation at S473 and T308; reverse phase protein array) and drug sensitivity (defined by the area under the curve; AUC) from the GDSC1 and CCLE databases. Associations between PI3K isoforms, AKT phosphorylation, and drug sensitivities were reported by fitting univariable and multivariable linear regression models with and without interaction terms to communicate the effects of AKT phosphorylation conditional on PIK3CB levels. We found that AKT phosphorylation and PIK3CB mRNA data together performed better as a biomarker in predicting therapeutic response to p110β-selective inhibitors than each variable alone, specifically we found that AKT phosphorylation at T308 was negatively related to p110β-selective inhibitor AZD6482 sensitivity at low PIK3CB expression levels (B = -0.069, p = 0.0513) and this relationship disappeared at higher expression levels (B = 0.04, p = 0.176) with an interaction at near statistical significance (p = 0.0674). We found that PIK3CB mRNA levels were significantly positively associated with TMZ resistance in GBM (B=0.019, p=0.0211) while other PI3K isoforms were not. While AKT phosphorylation is currently used as a biomarker for PI3K pathway inhibitors, in this study, we demonstrate that both PIK3CB mRNA and AKT phosphorylation together was a significant biomarker in sensitivity to p110β inhibitors as compared to assessing each independently. Furthermore, PIK3CB was implicated in TMZ resistance in GBM as compared to other catalytic isoforms.
NCOG-41. INTEGRATING NEUROPSYCHOLOGICAL CARE INTO A PEDIATRIC LONG-TERM SURVIVORSHIP CLINIC
Authors: Colleen Hess
Journal: Neuro-Oncology (2022)

Abstract Pediatric cancer survivors are vulnerable to neurocognitive deficits due to their treatment history including chemotherapy and radiation therapy. These treatments are associated with damage to the brain’s white matter pathways, contributing to neurocognitive “late effects” such as deficits in processing speed, working memory, executive function, visuospatial abilities, and fine motor skills. However, these neurocognitive deficits may go undiagnosed and therefore unsupported due to difficulties accessing neuropsychological care. This study seeks to improve survivors’ access to care, thereby increasing the likelihood of patients obtaining educational and therapeutic supports when needed, by integrating brief neuropsychological screenings into an existing medical clinic. During survivors’ annual oncology clinic visit, patients were administered a neurocognitive screening battery to assess their working memory, processing speed, and executive functions and thereby determine which patients would benefit from more comprehensive neuropsychological testing. The current sample of 22 patients (55% female) ranges from 6 to 21 years of age (M = 14). Based on testing performance, 23% of the sample (n = 5) demonstrated neurocognitive deficits according to the Neuropsychological Impairment Rule (NIR), and therefore was referred for more comprehensive neuropsychological assessment. Additionally, 9% of the sample (n = 2) was referred for further assessment, despite not meeting the NIR threshold, due to report of academic concerns. Importantly, 68% of the sample (n = 15) did not meet the NIR threshold and did not endorse neurocognitive concerns, and therefore did not require referral for further neuropsychological assessment. Current results demonstrate the utility of integrating neuropsychological care into long-term survivorship clinics via a neurocognitive screening battery as the majority of patients did not evidence significant deficits and therefore were adequately served from a neuropsychological lens without requiring additional assessment. In addition to increasing access to care, these efforts help to preserve families’ resources and reduce waitlists for patients in need.
CTNI-16. NRG-RTOG 9802 OBSERVATION ARM - LONG TERM RESULT
Authors: Fabio Iwamoto, Mei-Yin Polley, Edward Shaw, Jan Buckner, Geoffrey Barger, Stephen Coons, Peter Ricci, Mark Gilbert, Paul Brown, Keith Stelzer, C Leland Rogers, John Suh, Christopher Schultz, Steven Howard, Barbara Fisher, Michelle Kim, Jiayi Huang, Michael Haddock, Minhee Won, Minesh Mehta
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Radiation Therapy Oncology Group 9802 was a phase III trial for patients with centrally confirmed LGG (WHO grade II). Participants ³ 40 years or those with neurosurgeon defined less than gross total resection (GTR) were randomized to radiotherapy (RT) +/- PCV. In a separate cohort, adults age &amp;lt; 40 years with neurosurgeon defined GTR were observed by MRI every 6 months without adjuvant therapy. At last report, outcome for the observation cohort was immature with median follow-up of only 4.4 years. Here, we present mature outcomes for the observation arm. METHODS Eligible adults (as above) were observed by MRI every 6 months. OS and PFS were estimated by Kaplan-Meier method and estimated hazard ratios to characterize the prognostic variables. RESULTS There were 111 eligible patients (median age 30; median KPS = 100). Median follow-up was 16.1 years with 71 (64%) alive at the last follow-up. 79 patients (71%) had progressed with median PFS of 6.9 years. 5, 10, and 15 year-PFS and OS rates were 54%, 39%, 28% and 94%, 77%, and 65%. 1p19q status was codeleted in 32%, IDH1/2 mutant in 78% and MGMT promoter methylated in 39% of tested cases. Multivariate Cox analyses showed that preoperative tumor size ³ 4 cm (HR = 2.43 for PFS, p = 0.001; HR = 2.58 for death, p = 0.016) and residual disease on imaging ³ 1 cm (HR = 2.97 for PFS, P &amp;lt; 0.001; HR = 2.02 for death, p = 0.05) were associated with worse outcomes. Analyses based on molecular results will be presented. CONCLUSION A subset of low-grade gliomas can be observed after the initial resection based on younger age, smaller tumor size, and no residual disease on neuroimaging. This can likely be further refined by prognostic molecular markers. Patients with the most favorable prognostic factors can avoid or delay the acute and long-term side effects of RT and chemotherapy for several years.
CTNI-19. A TWO-PART, PHASE 1 STUDY OF RHENIUM-186 NANOLIPOSOME (186RNL) DELIVERED BY CONVECTION ENHANCED DELIVERY (CED) FOR RECURRENT OR PROGRESSIVE CHILDHOOD EPENDYMOMA AND HIGH-GRADE GLIOMA (HGG)
Authors: Ashley Plant-Fox, Michael DeCuypere, Sandi Lam, Carla Quijano, Lisa Sereno, Ande Bao, Norman LaFrance, Marc Hedrick, Andrew Brenner
Journal: Neuro-Oncology (2022)

Abstract Childhood ependymoma and HGG are difficult tumors to treat. Recurrent ependymoma is treated with re-resection and multiple rounds of external beam radiation therapy (EBRT). HGG is treated with chemoradiation followed by clinical trials, if available. While EBRT remains a central component of management, it is limited by tolerance of the surrounding normal brain tissue. Rhenium-186 NanoLiposome (186RNL) permits the selective delivery of beta-emitting radiation with excellent tumor retention. In an adult Phase 1 trial for recurrent glioblastoma (NCT01906385), the mean absorbed dose to the tumor was 392 Gy (CI 306 – 478), markedly higher than absorbed doses typically delivered by EBRT. Despite this, no dose-limiting toxicity was observed and no treatment-related serious adverse events have occurred. Here, we describe the first pediatric trial using a two-part, Phase 1 dose-finding study followed by expansion cohorts to explore efficacy. Enrolling subjects will be 6 to 21 years of age with a diagnosis of recurrent ependymoma or HGG. Subjects will be allowed to enroll either if they have exhausted standard of care options or if they are clinically stable and surgical resection can be deferred by 4 weeks. Part 1 will enroll up to 24 subjects to determine the maximum feasible dose (MFD) of 186RNL administered by CED. Tumor size and concentration of infusate will be escalated in each cohort (A-D) to a maximum tumor diameter of 6 cm (114.1 mL) and a concentration of 2mCi/ml. Up to 4 CED catheters will be used. Part 2 will independently evaluate 186RNL in 2 different expansion cohorts: Cohort 2A: recurrent ependymoma; Cohort B: recurrent HGG. The primary endpoint for Cohort 2A is overall response rate (ORR) by Radiographic Assessment in Pediatric Neuro-Oncology (RAPNO) criteria and the primary endpoint for Cohort 2B is progression free survival. Planned enrollment will begin in early 2023.
STEM-26. ASTROCYTIC SOX2+ CELLS RELAY IN NON-CANONICAL GLI SIGNALING TO FACILITATE MEDULLOBLASTOMA RELAPSE
Authors: Marzena Swiderska-Syn, Julia Mir-Pedrol, Alexander Oles, Benjamin Babcock, Vanesa Martin, Carsten Krieg, Timothy Gershon, Heather McCrea, Jezabel Rodriguez-Blanco
Journal: Neuro-Oncology (2022)

Abstract Medulloblastoma is the most common malignant pediatric brain tumor. Despite the fair efficacy of current treatment approaches, 30 % of patients with medulloblastoma relapse. Cells expressing the stemness biomarker SRY (sex determining region Y)-box 2 (SOX2) are known to play key roles in sustaining medulloblastoma growth, providing chemo-resistance, and driving tumor relapse. It is therefore critical to elucidate the underlying mechanisms that propagate these cells and ensure therapies to target them. Single cell sequencing analyses revealed the existence of a subset of astrocyte-like SOX2+ cells expressing biomarkers indicative of SHH signaling activation. Intriguingly, such SOX2+ cells were not affected by the upstream SHH inhibitor vismodegib. Using SOX2+ enriched cultures, we observed that astrocyte-like SOX2 cells not only express SHH effectors, but require GLI signaling to proliferate, and that GLI is activated in a non-canonical and MYC dependent manner. Importantly, in vivo inhibition of SHH signaling downstream of SMO depleted the vismodegib resistant SOX2+ cell pool, while reduced the ability of residual medulloblastoma tissues to engraft in vivo. Our data show that in medulloblastoma, a subset of SOX2+ tumor cells rely on non-canonical GLI signaling to propagate, and emphasizes the importance of using therapies that deplete SOX2+ cells to prevent tumor recurrence.
EPCO-08. CONSERVED FEATURES OF TERT PROMOTER DUPLICATIONS REVEAL AN ACTIVATION MECHANISM THAT MIMICS HOTSPOT MUTATIONS IN CANCER
Authors: Abigail Suwala, Carter Barger, Katarzyna M Soczek, Albert S Wang, Min Y Kim, Chibo Hong, Jennifer A Doudna, Susan M Chang, Joanna J Phillips, David A Solomon, Joseph F Costello
Journal: Neuro-Oncology (2022)

Abstract Mutations in the TERT promoter are the single most common non-coding mutation in cancer and represent the genetic underpinnings of tumor cell immortality. Beyond the two most common point mutations, G228A and G250A, which selectively recruit the ETS factor GABP to activate TERT, the significance of other variants in the TERT promoter are unknown. We identified duplications of wildtype sequence within the core promoter region of TERT in 7 different cancer types that have strikingly similar features including size, insertion position, and inclusion of one of the native ETS motifs. Each duplication activates the TERT promoter to a similar level as G228A and G250A and is critically dependent on the insertion site. The GABP tetramer binds to the TERT duplicated promoter sequence by virtue of the native ETS motif and its duplicated version with precise spacing, and it is necessary for the transcriptional activation by all duplications tested. Spatiotemporal analysis in a multifocal glioblastoma shows the duplication is clonal and its activation of TERT is readily detectable at the single cell level and in bulk tumor tissue. We conclude that recurrent TERT promoter duplications of the native ETS sequence are functionally and mechanistically equivalent to the hotspot mutations that confer tumor cell immortality. The shared mechanism of these divergent somatic genetic alterations suggests a strong selective pressure for recruitment of the GABP tetramer to activate TERT.
NIMG-31. CLINICALLY RELIABLE DEEP LEARNING MODEL FOR DIFFERENTIATION OF GLIOBLASTOMA FROM SINGLE BRAIN METASTASIS: ESTIMATING UNCERTAINTY WITH DEEP ENSEMBLES
Authors: Yae Won Park, Sung Soo Ahn, Seung-Koo Lee
Journal: Neuro-Oncology (2022)

Abstract OBJECTIVES To develop a clinically reliable deep learning model to differentiate glioblastoma (GBM) from solitary brain metastasis by providing predictive uncertainty estimates. METHODS A total of 465 patients (300 GBM, 165 single brain metastasis) were enrolled in the institutional training set. Deep ensembles model based on Densenet121 (2D CNN) were trained on multiparametric MRI. The models were validated in the external validation set consisting of 143 patients (101 GBM, 42 single brain metastasis). The classification performance was estimated, and entropy values for each input were evaluated for uncertainty measurement. Based on entropy values, the institutional training and external validation set were split to high and low uncertainty groups. To evaluate uncertainty on out-of-distribution data from unseen classes, 319 patients with meningiomas (from two external institutions) were separately tested in the deep ensemble model. RESULTS Deep ensembles showed an AUC, accuracy, sensitivity, and specificity of 0.82, 78.3%, 54.8%, and 88.1% on external validation in differentiating GBM from solitary brain metastasis. Deep ensembles showed higher performance in the low uncertainty group (AUC, accuracy, sensitivity, and specificity of 0.78, 89.0%, 62.5%, and 94.2%, respectively) than the high uncertainty group (AUC, accuracy, sensitivity, and specificity of 0.64, 65.5%, 51.4%, and 77.1%) according to entropy values on external validation. On out-of-distribution dataset of meningiomas, 292 (91.4%) patients were classified as high uncertainty group by deep ensembles whereas only 202 (63.4%) patients were classified into high uncertainty group by the single DenseNet121. CONCLUSIONS Not only can deep ensembles provide predictive uncertainty in differentiating GBM from single brain metastasis, but also avoid overconfident predictions in unseen classes and consequently offer reliable clinical decision making.
CTNI-26. SURGICAL WINDOW OF OPPORTUNITY TRIAL OF NAVTEMADLIN (KRT 232; AMG232) IN PATIENTS WITH RECURRENT GLIOBLASTOMA
Authors: Eudocia Lee, Michelle Rudek, Veronica Rendo, Nicholas Khuu, Tobias Walbert, Matthias Holdhoff, Frank Lieberman, Arati Desai, Roy Strowd, Emily Lapinskas, Kristine Pelton, William Pisano, Serena Desideri, Neeraja Danda, Joy Fisher, Xiaobu Ye, L Burt Nabors, Stuart Grossman, Rameen Beroukhim, Brian Alexander, Keith Ligon, Patrick Y Wen
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND KRT232 is an orally bioavailable, selective small molecule inhibitor of MDM2 that blocks the protein-protein interaction between MDM2 and p53. We performed a surgical window of opportunity trial of KRT232 in patients with recurrent GBM. METHODS The primary endpoint was to determine the tumor tissue concentration of KRT232. Prior to surgery, patients received KRT232 at either 120mg (n = 10, minimal dose that is consistently associated with alterations in serum MIC-1) or 240mg (n = 10; recommended phase 2 dose as monotherapy) for two days prior to surgical resection. Surgery was performed 3-6 hours following the last administration of KRT232. Tissue was analyzed for KRT232 concentration by LC/MS and for correlative studies. Participants with TP53 wild-type tumors were eligible to continue KRT232 following recovery from surgery at the RP2D of 240mg QD x 7 days q3weeks. RESULTS Twenty-one patients were enrolled from July 2018 to April 2020. One patient was deemed ineligible after surgery due to non-GBM tumor. Study met the prespecified criteria of target intra-tumor drug concentration of ≥ 25nM in contrast enhancing tissue in more than 50% of the patients in the 120mg cohort (67.1 ± 42.7nM in 8/10 patients) and 240mg (328.7 ± 468.1nM in 10/10 patients) cohort. Serum MIC-1 fold-changes from baseline (FCB) approximately 24 hours after a single dose of KRT232 were higher in the 240mg cohort (9.1 ± 4.1-FCB) than the 120mg cohort (3.6 ± 2.0-FCB). CDKN1A (p21), a downstream marker of p53, was significantly upregulated in analyzed participants whose GBM was TP53 wildtype, but not in TP53 mutant GBM or control samples (GBM treated with standard of care). CONCLUSION KRT232 at both 120mg and 240mg achieves adequate tumor tissue penetration and affects downstream pathways in TP53 wildtype GBM. The study has moved to Alliance to complete a phase 1 study of radiation + KRT232 in patients with newly diagnosed MGMT unmethylated GBM.
CNSC-19. GLIOMA-INDUCED NEURONAL REMODELING PROMOTES REGIONAL IMMUNOSUPPRESSION
Authors: Takahide Nejo, Saritha Krishna, Jacob S Young, Akane Yamamichi, Christian Jimenez, Tiffany Chen, Payal Watchmaker, Abrar Choudhury, David Diebold, Hirokazu Ogino, David Raleigh, Shawn L Hervey-Jumper, Hideho Okada
Journal: Neuro-Oncology (2022)

Abstract Gliomas remodel neuronal circuits and distinct intratumoral regions maintain functional connectivity through a subpopulation of synaptogenic malignant cells expressing Thrombospondin-1 (TSP-1, encoded by the Thbs1 gene). Single-cell RNA sequencing analyses of primary patient samples identified a significant downregulation of immune response in myeloid cells and lymphoid cells in high functionally connected intratumoral regions characterized by upregulated TSP-1. Understanding the functional significance of immunosuppression within functionally connected intratumoral regions may uncover therapeutic vulnerabilities. Here, we investigate glioma-neuronal-immune crosstalk across clinical tumor specimens and preclinical syngeneic models through bulk and single-cell RNA sequencing (13,670 cells), flow cytometry, and spatial transcriptomics. Using an SB28 murine glioma cell line with endogenous Thbs1 stably expressed, we generated a CRISPR Thbs1-knock-out (KO) cell line. Bulk RNA-sequencing demonstrated that Thbs1-WT tumors exhibited gene expression programming consistent with synapse-associated genes and synaptogenic factors, recapitulating enriched connectivity in primary patient samples. Flow cytometry of brain-infiltrating leukocytes revealed that macrophages isolated from Thbs1-KO tumors were more frequently polarized into the pro-inflammatory “M1-like” phenotype (median M1/M2 ratio = 0.6 [WT] vs 1.34 [KO], p &amp;lt; 0.006). Unbiased gene expression program analysis using spatial transcriptomics for in vivo tumor-harboring mouse brains demonstrated a significant spatial overlap of signatures of synaptogenesis (represented by Ntng1 and Nlgn3 genes) and downregulated immune response (represented by Nfkb1 and Cd83 genes). SB28-Thbs1-KO syngeneic models demonstrated slower tumor growth and significantly longer survival compared to Thbs1-WT counterparts (19 days [WT] vs 25 days [KO], p &amp;lt; 4.5E-5). The survival difference was abrogated in the B6-SCID immunodeficient mice, indicating the critical role of adaptive immunity in the survival advantage associated with TSP-1 inhibition. Our results identify previously unknown immunosuppression mechanisms in the context of glioma-induced intratumoral connectivity via Thbs1. Future therapeutic strategies targeting this glioma-neuronal-immune crosstalk may open up new avenues for glioblastoma immunotherapy.
DDDR-24. INTEGRATED ANALYSIS OF SINGLE CELL CHROMATIN ACCESSIBILITY AND RNA EXPRESSION IDENTIFIED COMMON VULNERABILITY DESPITE GLIOBLASTOMA HETEROGENEITY
Authors: Ramya Raviram, Anugraha Raman, Sebastian Preissl, Shaoping Wu, Tomoyuki Koga, Chenxu Zhu, Jens Luebeck, Kinsey Van Deynze, Jee Yun Han, Xioameng Hou, Zhen Ye, Anna Mischel, Yang Eric Li, Rongxin Fang, Tomas Baback, Joshua Mugford, Claudia Han, Christopher Glass, Cathy Barr, Paul Mischel, Vineet Bafna, Laura Escoubet, Bing Ren, Clark Chen
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION In 2021, the World Health Organization (WHO) reclassified glioblastoma, the most common form of adult brain cancer, into isocitrate dehydrogenase (IDH) wild-type glioblastomas and grade IV IDH mutant (G4 IDHm) astrocytomas. For both tumor types, intra-tumoral heterogeneity is a key contributor to therapeutic failure. METHODS we applied integrated genome-wide chromatin accessibility (snATACseq) and transcription (snRNAseq) profiles to clinical specimens derived IDHwt glioblastomas and G4 IDHm) astrocytomas, with goal of therapeutic target discovery. RESULTS The integrated analysis achieved resolution of intra-tumoral heterogeneity not previously possible, providing a molecular landscape of extensive regional and cellular variability. snATACseq delineated focal amplification down to an ~40 KB resolution. The snRNA analysis elucidated distinct cell types and cell states (neural progenitor/oligodendrocyte cell-like or astrocyte/mesenchymal cell-like) that were superimposable onto the snATACseq landscape. Paired-seq (parallel snATACseq and snRNAseq using the same clinical sample) provided high resolution delineation of extrachromosomal circular DNA (ecDNA), harboring oncogenes including CCND1 and EGFR. Importantly, the copy number of ecDNA genes correlated closely with the level of RNA expression. Integrated analysis across all specimens profiled suggests that IDHm grade 4 astrocytoma and IDHwt glioblastoma cells shared a common chromatin structure defined by open regions enriched for Nuclear Factor 1 transcription factors (NFIA and NFIB). Silencing of NF1A or NF1B suppressed in vitro and in vivo growth of patient-derived IDHwt glioblastomas and G4 IDHm astrocytoma models that mimic distinct glioblastoma cell states. CONCLUSION Our findings suggest despite distinct genotypes and cell states, glablastoma/G4 astrocytoma cells share dependency on core transcriptional programs, yielding an attractive platform for addressing therapeutic challenges associated with intra-tumoral heterogeneity.